The United Nations is under increasing pressure to set up an independent inquiry into its Syria aid programme after a Guardian investigation found contracts worth tens of millions of dollars have been awarded to people closely associated with the president, Bashar al-Assad.

Former UN officials, diplomats, lawyers, and the head of Human Rights Watch (HRW) are among those who have raised serious concerns about the way Damascus appears to be directing the aid effort and benefiting from some of these deals.

UN pays tens of millions to Assad regime under Syria aid programme

Read more

Salman Shaikh, a Middle East specialist who has worked for the UN, said it was time for the secretary general, Ban Ki-moon, to intervene. “It’s as serious as that,” he added.

The UN says its work has saved millions of lives. But it concedes it can only stay in Syria with the approval of Assad, who has restricted which partners its agencies are able to work with.

“Our choices in Syria are limited by a highly insecure context where finding companies and partners who operate in besieged and hard to reach areas is extremely challenging,” a UN spokesman said.

Analysis by the Guardian revealed UN agencies have been awarding substantial contracts to Syrian government departments and Syrian businessmen whose companies are under US and EU sanctions.

Documents show the World Health Organisation has spent more than $5m (£3.3m) to support Syria’s national blood bank, which is being controlled by Assad’s defence department, raising questions about whether blood supplies are reaching those in need or are being directed to the military first.

Syrians queue for water at a shelter in Hirjalleh, a rural area near the capital Damascus. Photograph: Xinhua / Barcroft Images

The UN’s own procurement documents show its agencies have done business with at least another 258 Syrian companies, paying sums as high as $54m and £36m. Many are likely to have links to Assad, or those close to him.

“In the name of delivering aid to some needy people in opposition-held areas, the UN is subsidising the Syrian government’s war-crimes strategy of targeting those same people,” said Kenneth Roth, executive director of HRW. “That’s hardly the tough-minded pragmatism that the UN claims is informing its aid efforts.”

Antonia Mulvey, the founder and executive director of Legal Action Worldwide, said the UN’s conduct was an example of “pragmatism versus principles playing out in a conflict. Upholding fundamental human rights loses nearly every time.”

The Syrian American Medical Society (SAMS), which runs more than 100 clinics in Syria, mostly in areas outside government control, told the Guardian that the Syrian defence ministry had tight control of kits at the country’s blood banks. “Activists and medical workers started to smuggle [supplies] to areas under siege and field hospitals,” said Dr Zaher Sahloul.

“It is shocking to find out the UN, through funding from the US and UK, have supported the regime’s blood banks while the same regime targeted, tortured and killed medics and activists who were trying to smuggle supplies to save the lives of the victims of regime atrocities.”

Shaikh, founder of the Shaikh Group, which promotes dialogue among the various parties in Syria, , said he had worked for the UN when its former secretary general, Kofi Annan, set up inquiries into Rwanda and the “oil for food” allegations.

“Ban Ki-moon now needs to do something similar here. Talking to Syrians, the mistrust and the lack of confidence regarding the UN’s efforts and particularly those inside the country is something that’s going to bedevil the whole international community for a very long time.

“We can’t condemn the UN totally – it is a complicated situation in Syria, which is why he needs to move fast to restore trust in the organisation. He needs to establish an inquiry with a mandate to investigate the facts of the system’s response to the humanitarian crisis in Syria, and it should cover the period March 2011 to December 2016.”

UN's $4bn aid effort in Syria is morally bankrupt | Reinoud Leenders

Read more

A senior European diplomat, who asked not to be named, said those countries with influence on Damascus had to put Assad under considerable political pressure to make it easier for the UN to operate in Syria. “It remains a reality that the UN can never be better than its member states, particularly the permanent members of the security council.”

The UN aid operation in Syria is the most expensive and complex it has ever undertaken. It argues it has already saved millions of lives during the brutal five-year conflict. Privately, officials fear if they over-challenge Assad the UN will be thrown out of the country.

“Operating in Syria, with the conflict now entering its sixth year, forces humanitarians to make difficult choices,” a UN spokesman said.

“When faced with having to decide whether to procure goods or services from businesses that may be affiliated with the government or let civilians go without life-saving assistance, the choice is clear: our duty is to the civilians in need.”

The UN also points out it does not have to abide by EU or US sanctions. It only needs to abide by UN sanctions.

The United Nations Children’s Emergency Fund (Unicef) said it had little choice but to work with the Syrian regime. “The alternative is stark: many more children dying or suffering. This is the dilemma that Unicef and humanitarian agencies face on a daily basis.

“Children in Syria are hurting because of the failure of politicians to reach a peaceful solution to the war. We cannot let them down. We must do everything to alleviate the suffering of children.”